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- PDB-2fbq: The crystal structure of transcriptional regulator PA3006 -

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Basic information

Entry
Database: PDB / ID: 2fbq
TitleThe crystal structure of transcriptional regulator PA3006
Componentsprobable transcriptional regulator
KeywordsTRANSCRIPTION / PA3006 / APC5893 / transcriptional regulator / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


positive regulation of protein secretion / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
PsrA, tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...PsrA, tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Transcriptional regulator PsrA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLunin, V.V. / Skarina, T. / Onopriyenko, O. / Kim, Y. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of transcriptional regulator PA3006
Authors: Lunin, V.V. / Skarina, T. / Onopriyenko, O. / Kim, Y. / Joachimiak, A. / Edwards, A.M. / Savchenko, A.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,0131
Polymers26,0131
Non-polymers00
Water4,360242
1
A: probable transcriptional regulator

A: probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)52,0262
Polymers52,0262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4330 Å2
ΔGint-47 kcal/mol
Surface area20570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.922, 70.141, 47.850
Angle α, β, γ (deg.)90.00, 111.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-243-

HOH

21A-296-

HOH

31A-359-

HOH

Detailsbiological assembly comes from asymmetric unit and symmetry related molecule (-x, y, -z)

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Components

#1: Protein probable transcriptional regulator


Mass: 26013.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 15598202, UniProt: Q9HZJ9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5K 25%, CaCl2 0.2M, Bis-Tris 0.1M, 2mM L-Cys, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793983 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793983 Å / Relative weight: 1
ReflectionResolution: 1.8→27.57 Å / Num. all: 23510 / Num. obs: 23510 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rsym value: 0.036 / Net I/σ(I): 36.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 2065 / Rsym value: 0.208 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.426 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23013 1220 5.2 %RANDOM
Rwork0.18287 ---
all0.18549 22229 --
obs0.18549 22229 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.96 Å2
2---0.05 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 0 242 1905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9592431
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15623.37383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71215323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7091514
X-RAY DIFFRACTIONr_chiral_restr0.1270.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021379
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2939
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21268
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.311.51144
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0421789
X-RAY DIFFRACTIONr_scbond_it3.1073712
X-RAY DIFFRACTIONr_scangle_it4.7254.5642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 60 -
Rwork0.228 1414 -
obs--84.66 %

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